This is not a Helix weakness IMHO, just a lot of flexibility and options. You can use the "stock" helix cab sim which sounds fine to my ears for most applications. You can load 3rd party IR's to specifically target tones you want, or you can use outboard gear (Two notes etc) for even more flexibility.
I have done all 3 and have had great results with each one. The 3rd party IR's are great for targeting specific tones, and I do like them. The only reason I use a 2 notes torpedo is because I already had it. It is in no way a piece of gear I would have felt compelled to buy because of some shortcoming in Helix.